GEO DataSets

(Submitter supplied) H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL9052

14 Samples

Download data: BED, SAM, TXT

(Submitter supplied) Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs co-transcriptionally and accurately reflects the advance of RNA polymerase II (Pol II). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: TSV

(Submitter supplied) Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification within transcribed regions, but it remains uncertain how these modifications influence, or are influenced by, properties of the elongation complex. Here we establish an intimate link between Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), and mono-ubiquitylation of histone H2B (H2Bub1), in the fission yeast Schizosaccharomyces pombe. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16218

6 Samples

Download data: GPR, TIFF

(Submitter supplied) Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and mutants is performed using Affymetrix IVT Arabidopsis ATH1 Genome Array.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL, CHP

(Submitter supplied) We compare patterns of H2Bub and H2B across genes in WT, ubp8 KO and Dot1 OE cells

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

12 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

24 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We identified that downregulation of RNF20/H2Bub1 is involved in HGSOC progression through altering key immune signaling pathways. The goal of ATAC-seq analysis was to profile chromatin conformation in FTSEC cells (FT190 and FT194 cell lines) with RNF20 knockdown (shRNF20) or control shRNA. The data generated by ATAC-Seq was integrated with RNA-seq data analysis for the same samples.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TXT

(Submitter supplied) We identified that downregulation of RNF20/H2Bub1 is involved in HGSOC progression through altering key immune signaling pathways. The goal of ATAC-seq analysis was to profile chromatin conformation in FTSEC cells (FT190 and FT194 cell lines) with RNF20 knockdown (shRNF20) or control shRNA. The data generated by ATAC-Seq was integrated with RNA-seq data analysis for the same samples.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

6 Samples

Download data: BIGWIG

(Submitter supplied) Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20584 GPL13988

24 Samples

Download data: BIGWIG

(Submitter supplied) The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to ensure proper mRNA maturation and prevent interference between neighboring genes. Pol II slowing downstream of the cleavage and polyadenylation signal (CPS) leads to recruitment of cleavage and polyadenylation factors and termination, but how this chain of events is initiated remains unclear. In a chemical-genetic screen we identified protein phosphatase 1 (PP1) isoforms as substrates of human positive transcription elongation factor b (P-TEFb), the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 complex. more...

Organism:

Schizosaccharomyces pombe

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13988 GPL20584

52 Samples

Download data: BEDGRAPH, BIGWIG, BW

(Submitter supplied) ChIP-chip of histone variants and modifications in A. thaliana WT and various mutants

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16218

26 Samples

Download data: GPR, TIFF

(Submitter supplied) The goal of the project was to study the effects on transctiptome of some mutations related with SAGA complex

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24365

4 Samples

Download data: TXT

(Submitter supplied) Chd1 is a conserved ATP-dependent chromatin remodeler that maintains the nucleosomal structure of chromatin, but the determinants of its specificity and its impact on gene expression are not well defined. To identify the determinants of Chd1 binding specificity in the yeast genome, we investigated Chd1 occupancy in mutants of several candidate factors. We found that several components of the PAF1 transcription elongation complex contribute to Chd1 recruitment to highly transcribed genes, and identified Spt4 as a factor that appears to negatively modulate Chd1 binding to chromatin. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

27 Samples

Download data: BW, TXT

(Submitter supplied) We report quantitative transcriptome data in WT and CHD1 mutant.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

4 Samples

Download data: TXT

(Submitter supplied) We report genome-wide Chd1 occupancy in WT and in ten elongation factor mutants, and genome-wide H3K4me3/H3K36me3 profiles in WT and CHD1 mutant.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

23 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112 GPL17021

25 Samples

Download data

(Submitter supplied) Gene body-associated monoubiquitination of H2B (H2Bub1) coupled with promoter-associated active histone modifications such as trimethylation H3 on lysine 4 (H3K4me3) and acetylation H3 on lysine 27 (H3K27ac) facilitate gene transcription. However, surprisingly, only a subset of genes is altered in their expression following knockdown of H2B ubiquitin-protein ligases RNF20 or RNF40 in human cells. In order to obtain a more complete genome- and transcriptome-wide understanding of the role of H2Bub1 in gene transcription, we generated tamoxifen-inducible Rnf40 knockout mouse embryonic fibroblasts (MEFs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Gene body-associated monoubiquitination of H2B (H2Bub1) coupled with promoter-associated active histone modifications such as trimethylation H3 on lysine 4 (H3K4me3) and acetylation H3 on lysine 27 (H3K27ac) facilitate gene transcription. However, surprisingly, only a subset of genes is altered in their expression following knockdown of H2B ubiquitin-protein ligases RNF20 or RNF40 in human cells. In order to obtain a more complete genome- and transcriptome-wide understanding of the role of H2Bub1 in gene transcription, we generated tamoxifen-inducible Rnf40 knockout mouse embryonic fibroblasts (MEFs). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

19 Samples

Download data: BIGWIG

(Submitter supplied) The experiment was designed to display differential gene expression profiling in one lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 cells upon knockdown of RNF20, by using RNAseq technology.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: TXT

(Submitter supplied) The estrogen receptor-alpha (ERα) determines breast cancer cell phenotype and is a prognostic indicator. A better understanding of the mechanisms controlling ERα function may uncover improved strategies for the treatment of breast cancer. Proteasome inhibition was previously reported to regulate estrogen-induced transcription but the mechanisms by which it influences ERα function remain controversial. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4090

Platform:

GPL14010

21 Samples

Download data: CEL